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Coexpression cluster:C2345: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.590005,1.03954,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,0.151681,0.706765,0.867962,0.905351,0.809319,0.532789,0.559384,1.05593,0.471262,1.67497,0.223552,0.581762,0.505745,0.731221,0.528529,0.632849,0.892087,0.316693,0.728867,0.537869,0.297585,0.682839,1.09415,1.10579,1.63198,1.23824,3.353,2.13139,0.740899,0.463978,0.971732,0.493145,0.66492,0.183156,0.53106,0.648765,0.61613,0.822818,0.694903,0.173425,0.538016,0.90714,0.83543,0.699149,1.17354,1.33024,0.812467,0.54284,0.777235,0.806003,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,2.7761,1.32819,0.893276,0.321165,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,2.34631,0.221873,3.0641,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,1.32435,0.456994,0.354969,1.15558,0.939507,2.11025,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,1.52945,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,2.51097,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,1.64086,1.37788,0.852645,1.52813,1.41398,0.676268,0.729481,3.26642,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.66252,3.0147,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,1.47036,0.997702,0.843324,0.423521,0.820225,0.644569
|tfbs_overrepresentation_jaspar=MA0003.1;6.11661,MA0004.1;0.71247,MA0006.1;0.532262,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;3.08565,MA0017.1;0.577281,MA0019.1;0.873355,MA0024.1;1.09684,MA0025.1;1.34373,MA0027.1;2.83281,MA0028.1;0.550763,MA0029.1;1.11704,MA0030.1;1.10506,MA0031.1;1.03735,MA0038.1;0.824639,MA0040.1;1.12314,MA0041.1;0.732902,MA0042.1;0.697662,MA0043.1;1.20635,MA0046.1;1.19471,MA0048.1;0.709734,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.396851,MA0056.1;0,MA0057.1;0.69331,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;1.01899,MA0061.1;0.360128,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;0.313194,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;0.866596,MA0074.1;0.819248,MA0076.1;0.623864,MA0077.1;1.16637,MA0078.1;0.926725,MA0081.1;0.604638,MA0083.1;1.21381,MA0084.1;1.72172,MA0087.1;1.17185,MA0088.1;0.536981,MA0089.1;0,MA0090.1;1.54523,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;0.535768,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;0.539569,MA0103.1;0.521546,MA0105.1;0.232357,MA0106.1;0.869173,MA0107.1;0.453492,MA0108.2;1.03412,MA0109.1;0,MA0111.1;0.655276,MA0113.1;0.886811,MA0114.1;0.447443,MA0115.1;1.45393,MA0116.1;0.457606,MA0117.1;1.24497,MA0119.1;0.586221,MA0122.1;1.27173,MA0124.1;1.41151,MA0125.1;1.32534,MA0130.1;0,MA0131.1;0.94608,MA0132.1;0,MA0133.1;0,MA0135.1;1.23748,MA0136.1;0.832277,MA0139.1;1.63368,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;1.70272,MA0146.1;0.481,MA0147.1;1.16748,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.931615,MA0035.2;0.778873,MA0039.2;0.777367,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;1.01696,MA0047.2;0.856092,MA0112.2;0.551048,MA0065.2;0.577908,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.229241,MA0155.1;0.533581,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;1.1691,MA0160.1;0.756582,MA0161.1;0,MA0162.1;0.0928415,MA0163.1;0.918944,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;2.72671,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0
}}
}}

Revision as of 20:35, 22 January 2013


Full id: C2345_optic_Neural_parietal_spinal_Myoblast_locus_globus



Phase1 CAGE Peaks

Hg19::chr15:68870949..68871019,+p3@CORO2B
Hg19::chr15:68871309..68871354,+p2@CORO2B
Hg19::chr15:68871361..68871409,+p1@CORO2B
Hg19::chr2:105470714..105470723,+p8@POU3F3


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
central nervous system9.22e-3381
nervous system6.34e-3289
neural plate9.29e-3282
presumptive neural plate9.29e-3282
structure with developmental contribution from neural crest1.22e-31132
cell layer1.56e-31309
epithelium2.04e-30306
neural tube6.15e-3056
neural rod6.15e-3056
future spinal cord6.15e-3056
neural keel6.15e-3056
brain1.01e-2868
future brain1.01e-2868
neurectoderm1.03e-2886
regional part of nervous system2.99e-2853
regional part of brain2.99e-2853
tube9.50e-27192
anatomical cluster1.45e-26373
ecto-epithelium1.31e-24104
multi-tissue structure6.57e-24342
anatomical conduit8.68e-24240
pre-chordal neural plate1.84e-2261
regional part of forebrain3.25e-2141
forebrain3.25e-2141
anterior neural tube3.25e-2141
future forebrain3.25e-2141
ectoderm-derived structure4.31e-20171
ectoderm4.31e-20171
presumptive ectoderm4.31e-20171
telencephalon4.88e-2034
brain grey matter6.61e-2034
gray matter6.61e-2034
cerebral hemisphere9.53e-1932
adult organism9.73e-19114
regional part of telencephalon9.77e-1932
anatomical system2.58e-16624
anatomical group5.38e-16625
paraxial mesoderm3.27e-1572
presumptive paraxial mesoderm3.27e-1572
dense mesenchyme tissue3.57e-1573
multi-cellular organism4.75e-15656
cerebral cortex7.61e-1525
pallium7.61e-1525
somite1.02e-1471
presomitic mesoderm1.02e-1471
presumptive segmental plate1.02e-1471
dermomyotome1.02e-1471
trunk paraxial mesoderm1.02e-1471
epithelial vesicle2.47e-1478
skeletal muscle tissue2.89e-1462
striated muscle tissue2.89e-1462
myotome2.89e-1462
muscle tissue5.90e-1464
musculature5.90e-1464
musculature of body5.90e-1464
regional part of cerebral cortex1.68e-1322
neocortex1.84e-1220
embryo2.40e-12592
developing anatomical structure1.10e-11581
multilaminar epithelium1.76e-1183
organ system subdivision4.33e-11223
vasculature2.57e-1078
vascular system2.57e-1078
embryonic structure3.81e-10564
mesenchyme5.58e-10160
entire embryonic mesenchyme5.58e-10160
posterior neural tube7.34e-1015
chordal neural plate7.34e-1015
germ layer7.75e-10560
germ layer / neural crest7.75e-10560
embryonic tissue7.75e-10560
presumptive structure7.75e-10560
germ layer / neural crest derived structure7.75e-10560
epiblast (generic)7.75e-10560
organ part1.22e-09218
artery1.36e-0942
arterial blood vessel1.36e-0942
arterial system1.36e-0942
splanchnic layer of lateral plate mesoderm2.59e-0983
trunk mesenchyme3.50e-09122
segmental subdivision of nervous system5.59e-0913
epithelial tube open at both ends1.37e-0859
blood vessel1.37e-0859
blood vasculature1.37e-0859
vascular cord1.37e-0859
systemic artery1.62e-0833
systemic arterial system1.62e-0833


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.16.11661
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.13.08565
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.10.69331
MA0058.10.605914
MA0059.10.604454
MA0060.11.01899
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.866596
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.11.54523
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.11.63368
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.11.70272
MA0146.10.481
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.20.931615
MA0035.20.778873
MA0039.20.777367
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.21.01696
MA0047.20.856092
MA0112.20.551048
MA0065.20.577908
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.533581
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.11.1691
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.918944
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.22.72671
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
ZNF263#1012748.221841637010680.0002187871180958320.00248476596637784



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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